There is probably no "right" or "wrong" answer for this. If a script is going to use 20 functions, it would certainly be more efficient to have all 20 of those functions in the same include file. However, if another script is going to use only one of those functions, it's going to be a waste of some time (both disk access and PHP processing) to load a file with 19 unused functions.
Generally, though, we're talking about milliseconds of difference (unless these are really big functions), so in general the best solution is the one that makes it easiest for you to maintain things.
Ultimately, if you move into the object-oriented techniques available in PHP, you can use your class files to organize things and set up an _autoload() function to automatically load class definitions when needed.
